Active spells should use real time instead of timestamps
Just cast any sustained spell to yourself and try to change the time via console:
set gamehour to X
or
set timescale to X
In OpenMW such changes affect real spell duration since we determine it using a spell casting timestamp, current timestamp and timescale:
end = start + effectDuration * timeScale / (60*60);
When the timescale is 0, spellcasting does not work at all.
Morrowind uses the real time do determine the spell time left, so if the spell should work 5 real seconds, it will work 5 real seconds.
So the suggested solution is to use the real time during spell update, but I am not sure what to do with spells from savegames since we store only spell casting timestamp.